Merge pull request #15 from mschauer/refactor2

Refactor
mschauer · Jan 30, 2020 · bad06bb · bad06bb
2 parents 25e9533 + 4b262ea
commit bad06bb
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Showing 84 changed files with 248 additions and 1,204 deletions.
diff --git a/Project.toml b/Project.toml
@@ -21,17 +21,17 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
 
 [compat]
-Bridge = "0.10"
-DataFrames = "0.20" 
+Bridge = "0.10, 0.11"
+DataFrames = "0.20"
 Distributions = "0.22"
 ForwardDiff = "0.10"
 GaussianDistributions = "0.3"
 JLD = "0.9"
 PDMats = "0.9"
 Plots = "0.28"
 RecursiveArrayTools = "2.0"
-StaticArrays = "0.12"
-TimerOutputs = "0.5" 
+StaticArrays = "0.11, 0.12"
+TimerOutputs = "0.5"
 julia = "1"
 
 [extras]

diff --git a/src/data-stefan/cardiac.npy → data-stefan/cardiac.npy b/src/data-stefan/cardiac.npy → data-stefan/cardiac.npy
diff --git a/src/data-stefan/cc.npy → data-stefan/cc.npy b/src/data-stefan/cc.npy → data-stefan/cc.npy
diff --git a/src/data-stefan/explanation.pdf → data-stefan/explanation.pdf b/src/data-stefan/explanation.pdf → data-stefan/explanation.pdf
diff --git a/src/data-stefan/match.npy.npz → data-stefan/match.npy.npz b/src/data-stefan/match.npy.npz → data-stefan/match.npy.npz
diff --git a/src/experiments/exp-cardiac/an_cardiac.jl → experiments/exp-cardiac/an_cardiac.jl b/src/experiments/exp-cardiac/an_cardiac.jl → experiments/exp-cardiac/an_cardiac.jl
diff --git a/src/experiments/exp-cardiac/cardiac.npy → experiments/exp-cardiac/cardiac.npy b/src/experiments/exp-cardiac/cardiac.npy → experiments/exp-cardiac/cardiac.npy
diff --git a/src/experiments/exp-cardiac/data_cardiac.jld → experiments/exp-cardiac/data_cardiac.jld b/src/experiments/exp-cardiac/data_cardiac.jld → experiments/exp-cardiac/data_cardiac.jld
diff --git a/src/experiments/exp-cardiac/gen_cardiac.jl → experiments/exp-cardiac/gen_cardiac.jl b/src/experiments/exp-cardiac/gen_cardiac.jl → experiments/exp-cardiac/gen_cardiac.jl
diff --git a/...xperiments/exp-cardiac/makefigs_cardiac.R → experiments/exp-cardiac/makefigs_cardiac.R b/...xperiments/exp-cardiac/makefigs_cardiac.R → experiments/exp-cardiac/makefigs_cardiac.R
diff --git a/src/experiments/exp-dgs/an_exp-dgs.jl → experiments/exp-dgs/an_exp-dgs.jl b/src/experiments/exp-dgs/an_exp-dgs.jl → experiments/exp-dgs/an_exp-dgs.jl
diff --git a/src/experiments/exp-dgs/data_exp-dgs.jld → experiments/exp-dgs/data_exp-dgs.jld b/src/experiments/exp-dgs/data_exp-dgs.jld → experiments/exp-dgs/data_exp-dgs.jld
diff --git a/src/experiments/exp-dgs/gen_exp-dgs.jl → experiments/exp-dgs/gen_exp-dgs.jl b/src/experiments/exp-dgs/gen_exp-dgs.jl → experiments/exp-dgs/gen_exp-dgs.jl
diff --git a/src/experiments/exp-dgs/makefigs_exp-dgs.R → experiments/exp-dgs/makefigs_exp-dgs.R b/src/experiments/exp-dgs/makefigs_exp-dgs.R → experiments/exp-dgs/makefigs_exp-dgs.R
diff --git a/src/experiments/exp-dgs/match.npy.npz → experiments/exp-dgs/match.npy.npz b/src/experiments/exp-dgs/match.npy.npz → experiments/exp-dgs/match.npy.npz
diff --git a/...experiments/exp0/animate_introexample.mp4 → experiments/exp0/animate_introexample.mp4 b/...experiments/exp0/animate_introexample.mp4 → experiments/exp0/animate_introexample.mp4
diff --git a/src/experiments/exp0/exp0.jl → experiments/exp0/exp0.jl b/src/experiments/exp0/exp0.jl → experiments/exp0/exp0.jl
@@ -19,8 +19,9 @@ Random.seed!(3)
 
 workdir = @__DIR__
 cd(workdir)
-include(dirname(dirname(workdir))*"/postprocessing.jl")
-outdir = workdir*("/")
+include(joinpath(BL.dir(),"scripts", "postprocessing.jl"))
+outdir = workdir
+mkpath(joinpath(outdir, "forward"))
 
 model = [:ms, :ahs][1]
 T = 1.0; dt = 0.005; t = 0.0:dt:T; tt_ =  tc(t,T)
@@ -55,7 +56,7 @@ xobsT =[ BL.q(Xf.yy[end])] # [Xf.yy[end].q[i] for i in 1:n ]
 
 Xfsave = []# typeof(zeros(length(tt_) * P.n * 2 * d * nshapes))[]
 push!(Xfsave, BL.convert_samplepath(Xf))
-write_mcmc_iterates(Xfsave, tt_, n, nshapes, [1], outdir*"forward/")
+write_mcmc_iterates(Xfsave, tt_, n, nshapes, [1], joinpath(outdir,"forward"))
 
 #--------- MCMC tuning pars ---------------------------------------------------------
 
@@ -91,8 +92,9 @@ xobs0 = BL.q(x0)
 #priorθ = product_distribution(fill(Exponential(1.0),3))
 priorθ = product_distribution([Exponential(ainit), Exponential(cinit), Exponential(γinit)])
 κ = 100.0
-prior_momenta = MvNormalCanon(gramkernel(xobs0,P)/κ)
-logpriormom(x0) = logpdf(prior_momenta, vcat(BL.p(x0)...))# +logpdf(prior_positions, vcat(BL.q(x0)...))
+priormom = prior_momenta = MvNormalCanon(gramkernel(xobs0,P)/κ)
+#logpriormom(x0) = logpdf(prior_momenta, vcat(BL.p(x0)...))# +logpdf(prior_positions, vcat(BL.q(x0)...))
+
 
 #########################
 
@@ -104,7 +106,7 @@ start = time() # to compute elapsed time
     Xsave, parsave, objvals, accpcn, accinfo, δ, ρ, covθprop =
     lm_mcmc(tt_, (xobs0,xobsT), Σobs, mT, P,
               obs_atzero, fixinitmomentato0, ITER, subsamples,
-              xinit, tp, priorθ, logpriormom, updatescheme,
+              xinit, tp, priorθ, priormom, updatescheme,
             outdir)
 elapsed = time() - start
 
@@ -114,9 +116,9 @@ perc_acc_pcn = mean(accpcn)*100
 println("Acceptance percentage pCN step: ", round(perc_acc_pcn;digits=2))
 write_mcmc_iterates(Xsave, tt_, n, nshapes, subsamples, outdir)
 write_info(model,ITER, n, tt_, updatescheme, Σobs, tp, ρ, δ, perc_acc_pcn, elapsed, outdir)
-write_acc(accinfo,accpcn,nshapes,outdir)
+write_acc(accinfo, accpcn, nshapes, outdir)
 
 v0 = Vector(xobs0)
 vT = [Vector(xobsT[1])]
 write_observations(v0, vT, n, nshapes, x0,outdir)
-write_noisefields(P,outdir)
+write_noisefields(P, outdir)
diff --git a/src/experiments/exp0/landmarks_evolution.pdf → experiments/exp0/landmarks_evolution.pdf b/src/experiments/exp0/landmarks_evolution.pdf → experiments/exp0/landmarks_evolution.pdf
diff --git a/src/experiments/exp0/makefigs_exp0.R → experiments/exp0/makefigs_exp0.R b/src/experiments/exp0/makefigs_exp0.R → experiments/exp0/makefigs_exp0.R
diff --git a/src/experiments/exp1-1D/an_exp1-1D.jl → experiments/exp1-1D/an_exp1-1D.jl b/src/experiments/exp1-1D/an_exp1-1D.jl → experiments/exp1-1D/an_exp1-1D.jl
@@ -12,17 +12,21 @@ using DelimitedFiles
 using CSV
 using StaticArrays
 using LinearAlgebra
-using JLD
+using JLD2
+using FileIO
 
 Random.seed!(9)
 
+
 workdir = @__DIR__
 cd(workdir)
-include(dirname(dirname(workdir))*"/postprocessing.jl")
-outdir = workdir*("/")
+include(joinpath(BL.dir(),"scripts", "postprocessing.jl"))
+outdir = workdir
+mkpath(joinpath(outdir, "forward"))
+
 
 #-------- read data ----------------------------------------------------------
-dat = load("data_exp1-1D.jld")
+dat = load("data_exp1-1D.jld2")
 xobs0 = dat["xobs0"]
 xobsT = dat["xobsT"]
 n = dat["n"]

diff --git a/src/experiments/exp1-1D/data_exp1-1D.jld → experiments/exp1-1D/data_exp1-1D.jld b/src/experiments/exp1-1D/data_exp1-1D.jld → experiments/exp1-1D/data_exp1-1D.jld
diff --git a/src/experiments/exp1-1D/gen_exp1-1D.jl → experiments/exp1-1D/gen_exp1-1D.jl b/src/experiments/exp1-1D/gen_exp1-1D.jl → experiments/exp1-1D/gen_exp1-1D.jl
@@ -6,7 +6,7 @@ using Random
 using Distributions
 using StaticArrays
 using LinearAlgebra
-using JLD
+using JLD2
 
 workdir = @__DIR__
 println(workdir)
@@ -31,4 +31,4 @@ xobs0 = x0.q
 xobsT = [exp.(xobs0[i])  for i in 1:n ]
 #xobsT = [PointF(1.0), PointF(0.4)]
 
-save("data_exp1-1D.jld", "xobs0",xobs0, "xobsT", xobsT, "n", n, "x0", x0, "nshapes", nshapes)
+JLD2.@save "data_exp1-1D.jld2" xobs0 xobsT n x0 nshapes
diff --git a/src/experiments/exp1-1D/makefigs_exp1-1D.R → experiments/exp1-1D/makefigs_exp1-1D.R b/src/experiments/exp1-1D/makefigs_exp1-1D.R → experiments/exp1-1D/makefigs_exp1-1D.R
diff --git a/src/experiments/exp1-ckl/an_exp1-ckl.jl → experiments/exp1-ckl/an_exp1-ckl.jl b/src/experiments/exp1-ckl/an_exp1-ckl.jl → experiments/exp1-ckl/an_exp1-ckl.jl
diff --git a/src/experiments/exp1-ckl/data_exp1-ckl.jld → experiments/exp1-ckl/data_exp1-ckl.jld b/src/experiments/exp1-ckl/data_exp1-ckl.jld → experiments/exp1-ckl/data_exp1-ckl.jld
diff --git a/src/experiments/exp1-ckl/data_exp1ckl.jld → experiments/exp1-ckl/data_exp1ckl.jld b/src/experiments/exp1-ckl/data_exp1ckl.jld → experiments/exp1-ckl/data_exp1ckl.jld
diff --git a/src/experiments/exp1-ckl/gen_exp1-ckl.jl → experiments/exp1-ckl/gen_exp1-ckl.jl b/src/experiments/exp1-ckl/gen_exp1-ckl.jl → experiments/exp1-ckl/gen_exp1-ckl.jl
diff --git a/src/experiments/exp1-ckl/makefigs_exp1-ckl.R → experiments/exp1-ckl/makefigs_exp1-ckl.R b/src/experiments/exp1-ckl/makefigs_exp1-ckl.R → experiments/exp1-ckl/makefigs_exp1-ckl.R
diff --git a/.../exp1-ckl/ms-parsestimated/acceptance.pdf → .../exp1-ckl/ms-parsestimated/acceptance.pdf b/.../exp1-ckl/ms-parsestimated/acceptance.pdf → .../exp1-ckl/ms-parsestimated/acceptance.pdf
diff --git a/...ckl/ms-parsestimated/bridges-overlaid.pdf → ...ckl/ms-parsestimated/bridges-overlaid.pdf b/...ckl/ms-parsestimated/bridges-overlaid.pdf → ...ckl/ms-parsestimated/bridges-overlaid.pdf
diff --git a/...exp1-ckl/ms-parsestimated/noisefields.csv → ...exp1-ckl/ms-parsestimated/noisefields.csv b/...exp1-ckl/ms-parsestimated/noisefields.csv → ...exp1-ckl/ms-parsestimated/noisefields.csv
diff --git a/...nts/exp1-translated/an_exp1-translated.jl → ...nts/exp1-translated/an_exp1-translated.jl b/...nts/exp1-translated/an_exp1-translated.jl → ...nts/exp1-translated/an_exp1-translated.jl
diff --git a/...s/exp1-translated/data_exp-translated.jld → ...s/exp1-translated/data_exp-translated.jld b/...s/exp1-translated/data_exp-translated.jld → ...s/exp1-translated/data_exp-translated.jld
diff --git a/.../exp1-translated/data_exp1-translated.jld → .../exp1-translated/data_exp1-translated.jld b/.../exp1-translated/data_exp1-translated.jld → .../exp1-translated/data_exp1-translated.jld
diff --git a/...ts/exp1-translated/gen_exp1-translated.jl → ...ts/exp1-translated/gen_exp1-translated.jl b/...ts/exp1-translated/gen_exp1-translated.jl → ...ts/exp1-translated/gen_exp1-translated.jl
diff --git a/...xp1-translated/makefigs_exp1-translated.R → ...xp1-translated/makefigs_exp1-translated.R b/...xp1-translated/makefigs_exp1-translated.R → ...xp1-translated/makefigs_exp1-translated.R
diff --git a/src/experiments/exp1/an_exp1.jl → experiments/exp1/an_exp1.jl b/src/experiments/exp1/an_exp1.jl → experiments/exp1/an_exp1.jl
@@ -12,17 +12,21 @@ using DelimitedFiles
 using CSV
 using StaticArrays
 using LinearAlgebra
-using JLD
+using JLD2
+using FileIO
 
 Random.seed!(9)
 
 workdir = @__DIR__
 cd(workdir)
-include(dirname(dirname(workdir))*"/postprocessing.jl")
-outdir = workdir*("/")
+include(joinpath(BL.dir(),"scripts", "postprocessing.jl"))
+outdir = workdir
+mkpath(joinpath(outdir, "forward"))
+
+
 
 #-------- read data ----------------------------------------------------------
-dat = load("data_exp1.jld")
+dat = load("data_exp1.jld2")
 xobs0 = dat["xobs0"]
 xobsT = dat["xobsT"]
 n = dat["n"]
@@ -99,7 +103,7 @@ priormom = MvNormalCanon( vcat(BL.p(x0)...), gramkernel(x0.q,P)/κ)
 #########################
 xobsT = [xobsT]
 xinit = State(xobs0, zeros(PointF,P.n))
-mT = zeros(PointF,n)
+mT = zeros(PointF, n)
 
 start = time() # to compute elapsed time
     Xsave, parsave, objvals, accpcn, accinfo, δ, ρ, covθprop =
@@ -116,8 +120,8 @@ println("Acceptance percentage pCN step: ", round(perc_acc_pcn;digits=2))
 write_mcmc_iterates(Xsave, tt_, n, nshapes, subsamples, outdir)
 write_info(model,ITER, n, tt_, updatescheme, Σobs, tp, ρ, δ, perc_acc_pcn, elapsed, outdir)
 write_observations(xobs0, xobsT, n, nshapes, x0,outdir)
-write_acc(accinfo,accpcn,nshapes,outdir)
-write_params(parsave,0:ITER,outdir)
-write_noisefields(P,outdir)
+write_acc(accinfo, accpcn, nshapes,outdir)
+write_params(parsave, 0:ITER, outdir)
+write_noisefields(P, outdir)
 
 #show(to; compact = true, allocations = true, linechars = :ascii)
diff --git a/src/experiments/exp1/data_exp1.jld → experiments/exp1/data_exp1.jld b/src/experiments/exp1/data_exp1.jld → experiments/exp1/data_exp1.jld
diff --git a/experiments/exp1/data_exp1.jld2 b/experiments/exp1/data_exp1.jld2
diff --git a/src/experiments/exp1/gen_exp1.jl → experiments/exp1/gen_exp1.jl b/src/experiments/exp1/gen_exp1.jl → experiments/exp1/gen_exp1.jl
@@ -6,7 +6,7 @@ using Random
 using Distributions
 using StaticArrays
 using LinearAlgebra
-using JLD
+using JLD2
 
 workdir = @__DIR__
 println(workdir)
@@ -37,4 +37,4 @@ stretch = SMatrix{2,2}(1.0 + ψ, 0.0, 0.0, 1.0 - ψ)
 shift = [0.5, 0.0]
 xobsT = [rot * stretch * xobs0[i] + shift  for i in 1:n ]
 
-save("data_exp1.jld", "xobs0",xobs0, "xobsT", xobsT, "n", n, "x0", x0, "nshapes", nshapes)
+JLD2.@save "data_exp1.jld2" xobs0 xobsT n x0 nshapes
diff --git a/src/experiments/exp1/makefigs_exp1.R → experiments/exp1/makefigs_exp1.R b/src/experiments/exp1/makefigs_exp1.R → experiments/exp1/makefigs_exp1.R
diff --git a/src/experiments/exp1/ms/accdf.csv → experiments/exp1/ms/accdf.csv b/src/experiments/exp1/ms/accdf.csv → experiments/exp1/ms/accdf.csv
diff --git a/src/experiments/exp1/ms/acceptance.pdf → experiments/exp1/ms/acceptance.pdf b/src/experiments/exp1/ms/acceptance.pdf → experiments/exp1/ms/acceptance.pdf
diff --git a/src/experiments/exp1/ms/bridges-faceted.pdf → experiments/exp1/ms/bridges-faceted.pdf b/src/experiments/exp1/ms/bridges-faceted.pdf → experiments/exp1/ms/bridges-faceted.pdf
diff --git a/src/experiments/exp1/ms/bridges-overlaid.pdf → experiments/exp1/ms/bridges-overlaid.pdf b/src/experiments/exp1/ms/bridges-overlaid.pdf → experiments/exp1/ms/bridges-overlaid.pdf
diff --git a/src/experiments/exp1/ms/info.txt → experiments/exp1/ms/info.txt b/src/experiments/exp1/ms/info.txt → experiments/exp1/ms/info.txt
diff --git a/src/experiments/exp1/ms/iterates.csv → experiments/exp1/ms/iterates.csv b/src/experiments/exp1/ms/iterates.csv → experiments/exp1/ms/iterates.csv
diff --git a/src/experiments/exp1/ms/momenta-faceted.pdf → experiments/exp1/ms/momenta-faceted.pdf b/src/experiments/exp1/ms/momenta-faceted.pdf → experiments/exp1/ms/momenta-faceted.pdf
diff --git a/src/experiments/exp1/ms/noisefields.csv → experiments/exp1/ms/noisefields.csv b/src/experiments/exp1/ms/noisefields.csv → experiments/exp1/ms/noisefields.csv
diff --git a/src/experiments/exp1/ms/obs0.csv → experiments/exp1/ms/obs0.csv b/src/experiments/exp1/ms/obs0.csv → experiments/exp1/ms/obs0.csv
diff --git a/src/experiments/exp1/ms/scatter-pars.pdf → experiments/exp1/ms/scatter-pars.pdf b/src/experiments/exp1/ms/scatter-pars.pdf → experiments/exp1/ms/scatter-pars.pdf
diff --git a/src/experiments/exp1/ms/trace-pars.pdf → experiments/exp1/ms/trace-pars.pdf b/src/experiments/exp1/ms/trace-pars.pdf → experiments/exp1/ms/trace-pars.pdf
diff --git a/src/experiments/exp2/accdf.csv → experiments/exp2/accdf.csv b/src/experiments/exp2/accdf.csv → experiments/exp2/accdf.csv
diff --git a/src/experiments/exp2/acceptance.pdf → experiments/exp2/acceptance.pdf b/src/experiments/exp2/acceptance.pdf → experiments/exp2/acceptance.pdf
diff --git a/src/experiments/exp2/an_exp2.jl → experiments/exp2/an_exp2.jl b/src/experiments/exp2/an_exp2.jl → experiments/exp2/an_exp2.jl
@@ -10,14 +10,17 @@ using DelimitedFiles
 using CSV
 using StaticArrays
 using LinearAlgebra
-using JLD
+using JLD2
+using FileIO
 
 Random.seed!(9)
 
 workdir = @__DIR__
 cd(workdir)
-include(dirname(dirname(workdir))*"/postprocessing.jl")
-outdir = workdir*("/")
+include(joinpath(BL.dir(),"scripts", "postprocessing.jl"))
+outdir = workdir
+mkpath(joinpath(outdir, "forward"))
+
 
 #-------- read data ----------------------------------------------------------
 dat = load("data_exp2.jld")

diff --git a/src/experiments/exp2/bridges-faceted.pdf → experiments/exp2/bridges-faceted.pdf b/src/experiments/exp2/bridges-faceted.pdf → experiments/exp2/bridges-faceted.pdf
diff --git a/src/experiments/exp2/bridges-overlaid.pdf → experiments/exp2/bridges-overlaid.pdf b/src/experiments/exp2/bridges-overlaid.pdf → experiments/exp2/bridges-overlaid.pdf
diff --git a/src/experiments/exp2/data_exp2.jld → experiments/exp2/data_exp2.jld b/src/experiments/exp2/data_exp2.jld → experiments/exp2/data_exp2.jld
diff --git a/experiments/exp2/data_exp2.jld2 b/experiments/exp2/data_exp2.jld2
diff --git a/src/experiments/exp2/gen_exp2.jl → experiments/exp2/gen_exp2.jl b/src/experiments/exp2/gen_exp2.jl → experiments/exp2/gen_exp2.jl
@@ -6,7 +6,7 @@ using Random
 using Distributions
 using StaticArrays
 using LinearAlgebra
-using JLD
+using JLD2
 
 workdir = @__DIR__
 println(workdir)
@@ -41,4 +41,4 @@ end
 xobs0 = []
 
 
-save("data_exp2.jld", "xobs0",xobs0, "xobsT", xobsT, "n", n, "x0", x0, "nshapes", nshapes)
+JLD2.@save "data_exp2.jld2" xobs0 xobsT n x0 nshapes
diff --git a/src/experiments/exp2/info.txt → experiments/exp2/info.txt b/src/experiments/exp2/info.txt → experiments/exp2/info.txt
diff --git a/src/experiments/exp2/iterates.csv → experiments/exp2/iterates.csv b/src/experiments/exp2/iterates.csv → experiments/exp2/iterates.csv
diff --git a/src/experiments/exp2/makefigs_exp2.R → experiments/exp2/makefigs_exp2.R b/src/experiments/exp2/makefigs_exp2.R → experiments/exp2/makefigs_exp2.R
diff --git a/src/experiments/exp2/momenta-faceted.pdf → experiments/exp2/momenta-faceted.pdf b/src/experiments/exp2/momenta-faceted.pdf → experiments/exp2/momenta-faceted.pdf
diff --git a/src/experiments/exp1-try/an_exp1-try.jl → ...iments/inprogress/exp1-try/an_exp1-try.jl b/src/experiments/exp1-try/an_exp1-try.jl → ...iments/inprogress/exp1-try/an_exp1-try.jl
diff --git a/src/experiments/exp1-try/data_exp1-try.jld → ...nts/inprogress/exp1-try/data_exp1-try.jld b/src/experiments/exp1-try/data_exp1-try.jld → ...nts/inprogress/exp1-try/data_exp1-try.jld
diff --git a/src/experiments/exp1-try/forwardhalfway.jld → ...ts/inprogress/exp1-try/forwardhalfway.jld b/src/experiments/exp1-try/forwardhalfway.jld → ...ts/inprogress/exp1-try/forwardhalfway.jld
diff --git a/src/experiments/exp1-try/gen_exp1-try.jl → ...ments/inprogress/exp1-try/gen_exp1-try.jl b/src/experiments/exp1-try/gen_exp1-try.jl → ...ments/inprogress/exp1-try/gen_exp1-try.jl
diff --git a/src/experiments/exp1-try/makefigs_exp1-try.R → ...s/inprogress/exp1-try/makefigs_exp1-try.R b/src/experiments/exp1-try/makefigs_exp1-try.R → ...s/inprogress/exp1-try/makefigs_exp1-try.R
diff --git a/src/experiments/prior/prior_initpos.jl → ...riments/inprogress/prior/prior_initpos.jl b/src/experiments/prior/prior_initpos.jl → ...riments/inprogress/prior/prior_initpos.jl
diff --git a/scripts/generatedata.jl b/scripts/generatedata.jl
@@ -21,7 +21,7 @@ function generatedata(dataset,P,t,σobs)
     n = P.n
     if dataset=="forwardsimulated"
         q0 = [PointF(2.0cos(t), sin(t)) for t in (0:(2pi/n):2pi)[1:n]]  #q0 = circshift(q0, (1,))
-        p0 = [Point(1.0, -3.0) for i in 1:n]/n  # #p0 = [randn(Point) for i in 1:n]
+        p0 = [5*Point(1.0, -3.0) for i in 1:n]/n  # #p0 = [randn(Point) for i in 1:n]
         x0 = State(q0, p0)
         Wf, Xf = landmarksforward(t, x0, P)
         xobs0 = x0.q + σobs * randn(PointF,n)
@@ -50,8 +50,8 @@ function generatedata(dataset,P,t,σobs)
         obs_atzero = true
     end
     if dataset=="bear"
-        bear0 = readdlm(joinpath(@__DIR__,"data-stefan", "bear1.csv"), ',')
-        bearT = readdlm(joinpath(@__DIR__,"data-stefan", "bear2.csv"), ',')
+        bear0 = readdlm(joinpath(@__DIR__, "..", "data-stefan", "bear1.csv"), ',')
+        bearT = readdlm(joinpath(@__DIR__, "..", "data-stefan", "bear2.csv"), ',')
         nb = size(bear0)[1]
         avePoint = Point(414.0, 290.0)  # average of (x,y)-coords for bear0 to center figure at origin
         xobs0 = [Point(bear0[i,1], bear0[i,2]) - avePoint for i in 1:nb]/200.
@@ -94,7 +94,7 @@ function generatedata(dataset,P,t,σobs)
         obs_atzero = true
     end
     if dataset=="generatedstefan"
-        testshapes = npzread(joinpath(@__DIR__,"data-stefan", "match.npy.npz"))
+        testshapes = npzread(joinpath(@__DIR__, "..", "data-stefan", "match.npy.npz"))
         xobs0vec =  get(testshapes,"q0",0)
         xobsTvec =  get(testshapes,"v",0)
         p0vec = get(testshapes,"p",0)
@@ -155,7 +155,7 @@ function generatedata(dataset,P,t,σobs)
         # for i in range(N_samples):
         #      plt.plot(qs[i,:,0],qs[i,:,1])
 
-        cardiac = npzread(joinpath(@__DIR__,"data-stefan","cardiac.npy"))  # heart data (left ventricles, the one we used in https://arxiv.org/abs/1705.10943
+        cardiac = npzread(joinpath(@__DIR__, "..", "data-stefan","cardiac.npy"))  # heart data (left ventricles, the one we used in https://arxiv.org/abs/1705.10943
         cardiacx = cardiac[:,:,1]  # x-coordinates of landmarks
         cardiacy = cardiac[:,:,2]  # y-coordinates of landmarks
         nshapes = 14
@@ -189,7 +189,7 @@ function generatedata(dataset,P,t,σobs)
 end
 
 if false
-    cc = npzread(joinpath(@__DIR__,"data-stefan","cc.npy")) # corpus callosum data
+    cc = npzread(joinpath(@__DIR__, "..", "data-stefan","cc.npy")) # corpus callosum data
 
                     # there are 14 cardiac images, in https://arxiv.org/pdf/1705.10943.pdf 17 landmarks are chosen
 end
diff --git a/src/landmarkbridge_animation.jl → scripts/landmarkbridge_animation.jl b/src/landmarkbridge_animation.jl → scripts/landmarkbridge_animation.jl